From 133885f356d61f72bb7e51334c0183cbcf262c56 Mon Sep 17 00:00:00 2001 From: Sigve Nakken Date: Tue, 24 Sep 2024 11:21:16 +0200 Subject: [PATCH] 20240922 release --- R/sysdata.rda | Bin 1644 -> 1647 bytes data-raw/data-raw.R | 6 +++--- data-raw/gwas_utils.R | 10 ++++++++++ 3 files changed, 13 insertions(+), 3 deletions(-) diff --git a/R/sysdata.rda b/R/sysdata.rda index ae7092a32acccfe87aad675f63deb1f8eca9da9c..564477d91c8d5a33b2204ca522f2eb16d026284d 100644 GIT binary patch literal 1647 zcmV-#29WteT4*^jL0KkKS-Ov)XaEIo|HJ=#%p-7vf8c-r|M0*6|L{Tp2mk;C00Gbi zo)q_(fZ%s~)h_Q92Bev&VrizB5vk-OVrZV4nmrh&rjQvKH6A1Y0M#_fp-nSSRQ*pB zdZ&bXq3SdM83CX)00006sel3+X{n%Oqct#|rjJO_8Z;U-$N&bJ0M$R$RQ9GQWb~Rn zK*#{~4WeN*#54c{Lrnu3AW0!3Oqyw-GGZsG;DS9Tl)(c)XnH}Wg9Hbu`UGlL9*{u= z6oICM)4{-r82}a@<&dPD9W7LGsQ6-vvlB>_w}?tWM_0s>%m6JivNk@s-Uy@9L;o6_ zk_4uwcbrZwj3*ZQZAy?+fv!mW;P7CHAbhniy5&U=;rF4fGN{Y?7Bp~pcrC{Z)!`QX zGNyML+;gL+S0(nXU)yc1{+jjp>-ci2=nlX^5rhB%ln{gAun4boF+-^0&@u@ z4q+fmp|@EZtdPSA0o$h2s^HcV41z(Md6;Hv*>>5O280NW^#V!+>%h>jChtSEJUhQF zi8P;)l*A_;T8pVhH(&|`k4_UK4^dyr^EVM{D6G`%ef8Vr0)f&f1AjTmb6^j2tsJ>4 zj_MkPncUefNxpX!i+HCUXMBjZgAJKyXn?gPiJFJj-gHd*aTG}u(Ht0@zKmn%tjPl; z9p@Lcf-F_K)xi;4YnMR{j;vKFQln&+JW=K0t-nA8>eug5gUd5tvpr7EzDzJPP9zm^ z+coXN%=6GYv;q+7vj71#zo(pZaNnYD!#Zpg~D9q{Cw4I~6*V!_%P) zDHOcdo(dG{Q5&7+uGDGg^dVv7Vys|D#|tfMVwKwGvME6Br6u1g-sH*zASiN1*C#}z zE+H7=Jne;xBJ4X9V-{5Ay$D=j*``#v3WA75bJPF~G2C*Rh1BZKhrTChYl(?9F%6;> zhp~4sGgj7B00Sv(aYm7639+s-IWD$yLJVUeMNb80r0i7aVzD6;L==W?&E^sUfMv|i zF{5fVBC#A*K=w2D-lfT9L^}%LZcZvF1AzM(a&+6dqicJ$lXng%*L<_~Yv?+=Y4<9I z93Ao7o5u)R=m)YVE0L?EM8smYgBS%xuW81 zN7+r9kU2z{t;^hq~NSN!^OUoI`nJ<66=geEWceysLzoq{VTCDrt7o#S$VdgC?nH z#0|Rq0N~Z%N-UmXJdG)j31RGZX;|;HKWCB^7L|M$T5WxD?H` z86k(7$oV@w)yQLnmMZ5kp%oeiqnZ@`wxY{IN(>Ovu`!;)3X?!mCWz{2@7|i)D@lPE z=JYtEfB~NAEH2dhGQ^IW1|7*TLpdG+Ri6MTxEA=%R;fw}XIH4Aor@`aI`#3?7C_Lg z6q8Lct4hlp{F=pwm8tvP@l><;l9-YbLQ73Uf;gkN02m`|05bqE03O!g8)fIelNT01 zH0@*g_jq}tjy#<^239tXT;5JOy{TnLBb*z|uI9^OdY4K-D|*604hB|bZeI7))3op? zTsKDlTzjTJSXBc;qQ@G6*^Y8Bx*XXO7@&+q=SjIuQ)~>r;&?c#PnSxxJF%SGp{wAP z*1V6bjp={@a1e`DccytJFyJeM4c<0mL!)&xgKAhfd51)@n;g?=-HW5uEpdz&0OEP( z&xyoDF6XZs4AO%=hb9OHr#U^&2owO7cs){K9vLB)&26q4e literal 1644 zcmV-y29x!aGynrkKpLm|sUym5ModPY zqta;81Tq={lL??OOok9?wHgT|K{BV|O`s6eVW0%TG&Erv7!xDVPf?RkQ^*mGRP=%b z72*b-3F(2riCF*@J<9TX=+}1bB3k*nk4dD+6c#sdys4!$tkr z+>!*Rk0-27E(|9Y`|RCFBY?b0{g8MtP>?=pa@}@C2lVZ!tum39m{_^DhMzoK8`p zNtlunVMA(iX4_fD-=>49Q|FLK7^XyY^nW3IRO~1?Bf`Gq3)}>P9Dqb32bHZzS#Tmt zkGS)qI$Y1#jIjwV7oHW`+Xr?l)c{+sBy9O{laek%5scz_lvtvIWyUp?P86g%%_$PW4$yVVhM%#pxu3DgdhPun_(q;wIsQO1Q9;VWb zhD^U)6{csf{i;NMVG@V2rCNiBi*csYgqf$JTy6FpeS993LlMdE;QiiF&{{~YT5Mcr zmbFHw9T;gx%7kws`$HN*uv*)WZKvl&T{Evx@|{0i17}yJFh<%LVF^`;{j=8-y;&e& zzpS?Ep7IL3lFl#24K z(pqsq0000BMLHI&%XtcJtJ{2rn(MX;TBcWb5+Ijslhdj?9Bx36&?hgncLjOP27@`N zaIh2UI^ty5?azWkVQ0Mb$%KRt?3m(~ZrnY@tfqwz2`5X4_JBQL1XF$B3b-7KUTyju z@-<>m%1JaP78!Fcm0h`aXO!-KPK{Ev0=H2tNFoe_xP*W-z*kmq03Rp&^}AjSj1N!& z0EhtU=ruV?IajJtp_VnHQuCwKH=)6^&or1dxdposiA!=2qv*bkKo92Fz;TnXaB<%7 z=UysFh9#F>OKVny&P!2(4&B{6n$Mk7{vOAT(*OeFj%u?-G$L9VJGSaLieyer01W{N zR;L)K&U~gk8S3)*Q z zJGeTi^etwHB_@-rG2o0E6-)7eiX*dt?bqS=ML@-{7|qMsYR@4d(vx!L9g8`*XS<)F zP=e)Ht9S|wKm{4{(`*co;XsDsKLw(S0N}ZZ!b_O?Z;;-D-M3tUF%D;wrPZ%Q@BbOK>%Mdbn$qwHS_`8xR!i0mY!|*`i^#7#* diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R index 9758078..042ec93 100644 --- a/data-raw/data-raw.R +++ b/data-raw/data-raw.R @@ -6,8 +6,8 @@ source("data-raw/gwas_utils.R") options(timeout = 500000) -catalog_version_date <- '2024-08-12' -ebi_catalog_version_date <- '20240812' +catalog_version_date <- '2024-09-22' +ebi_catalog_version_date <- '20240922' fname_catalog_associations <- file.path( "data-raw", @@ -188,7 +188,7 @@ for (c in gwas_collections) { gwas_phenotype_records <- as.data.frame( gwas_hits[[c]] |> dplyr::left_join( - gwas_citations[[c]], + gwas_citations[[c]], by = "pmid", relationship = "many-to-many") |> dplyr::mutate(gwas_catalog_version = ebi_catalog_version_date) |> dplyr::mutate(p_value_verbose = sprintf("%2.1e",p_value)) |> diff --git a/data-raw/gwas_utils.R b/data-raw/gwas_utils.R index 10bfb67..4a8fb17 100644 --- a/data-raw/gwas_utils.R +++ b/data-raw/gwas_utils.R @@ -7,6 +7,16 @@ #' get_dbsnp_data <- function(rsids, cache_dbsnp_fname = NA){ + # gw_hits <- gwas_hits_pr_rsid$cancer |> + # dplyr::filter( + # stringr::str_detect(rsid, "^rs[0-9]{1,}")) |> + # tidyr::separate( + # gwas_hit, + # c("rsid","risk_allele","pmid","tag","p_value","efo_id"), + # sep = "\\|" + # ) + + rsids <- rsids[stringr::str_detect(rsids,"^rs[0-9]{1,}")] rsid_df <- data.frame('rsid' = rsids) cache_dbsnp <- data.frame()